Deborah Dean, MD, MPH

Professor Dean’s research involves in vitro and bioinformatic approaches along with studies of human populations to address host-pathogen interactions, including bacterial genomics, host immune responses and microbiota/microbiome/metabolome associations with disease protection and pathogenesis related to the obligate intracellular bacterium Chlamydia trachomatis. Her group was the first to identify genomic recombination in this human pathogen. The Dean lab also studies the evolution of zoonotic chlamydial species. Professor Dean’s international research focusses on trachoma and sexually transmitted disease populations in Nepal, India, Ecuador, Thailand, Vietnam and Fiji. In addition, her group collaborates with Bay Area biotech start-ups to develop vaccines and rapid inexpensive point-of-care diagnostics for C. trachomatis and Neisseria gonorrhoeae for global deployment. She has a track record of 33 years of uninterrupted funding from the National Institutes of Health in addition to grants from the U.S. Centers for Disease Control, World Health Organization and the National Science Foundation. She has also mentored over 170 national and international undergraduate, graduate and medical students, and postdoctoral fellows who have gone on to university professorships and positions at institutes of health and centers for disease control throughout the world. Professor Dean remains an advocate for ocular and reproductive health among vulnerable and neglected populations worldwide.
Education
2021 - UCSF Diversity, Equity and Inclusion Champion, University of California San Francisco School of Medicine
2019 - Diversity, Equity, and Inclusion Champion Training, University of California
Postdoctoral Fellow, 1991 - Microbial Pathogenesis, Stanford University School of Medicine
Clinical Fellow, 1989 - Infectious Diseases, Stanford University School of Medicine
MPH, 1986 - Epidemiology & Biostatistics, University of California Berkeley School of Public Health
Internship & Residency, 1985 - Straight Internal Medicine, University of California San Francisco School of Medicine
MD, 1982 - Medicine, Albert Einstein College of Medicine
B.S./B.A., 1977 - Environmental Sciences/Philosophy, University of California Berkeley
Honors and Awards
  • Award for service and commitment as an Editorial Board Member, Public Library of Science, 2023
  • Scientific Career Achievement Award, University of California San Francisco School of Medicine, Benioff Children's Hospitals, 2020
  • Fellow, American Academy of Microbiology, American Academy of Microbiology, Washington, D.C., 2019
  • Influential Alumni Award for Significant Contributions in the Field of Public Health, University of California Berkeley, School of Public Health, 2018
  • Outstanding Mentorship Award, 16 years of service, NIH Minority Summer Student Research Program, 2016
  • United Nations Global Citizen Award, United Nations, 2009
  • Scientific Achievement Award for the most outstanding research, Children's Hospital Oakland Research Institute, 2006
  • Apple Cluster Workgroup for Bioinformatics Award, Apple Inc., Cupertino, CA, 2004
  • Award for excellence in mentoring graduate students, University of California Berkeley, School of Public Health, 2003
  • Member, Global Alliance to Eliminate Blinding Trachoma, World Health Organization, Geneva, Switzerland, 1999
  • Faculty Development Award, University of California San Francisco, School of Medicine, 1995
  • Physician Scientist Award, National Institutes of Health, 1990
  • Giannini Foundation Fellowship, Giannini Foundation, San Francisco, CA, 1989
  • McCormick Fund Award for Research Excellence, Stanford University School of Medicine, 1988
  • University of California Regents Scholar, University of California Berkeley, 1985
  1. Seth-Smith H, Bommana S, Dean D, Read TD, Marti H. Chlamydia suis undergoes interclade recombination promoting Tet-island exchange. BMC genomics 2024. PMID: 39060998




  2. Greub G, Pillonel T, Bavoil PM, Borel N, Campbell LA, Dean D, Hefty S, Horn M, Morré SA, Ouellette SP, Pannekoek Y, Puolakkainen M, Timms P, Valdivia R, Vanrompay D. Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae. New microbes and new infections 2023. PMID: 37416863





  3. Wongsamart R, Bhattarakasol P, Chaiwongkot A, Wongsawaeng D, Okada PA, Palaga T, Leelahavanichkul A, Khovidhunkit W, Dean D, Somboonna N. Multiplex recombinase polymerase amplification for high-risk and low-risk type HPV detection, as potential local use in single tube. Scientific Reports 2023. PMID: 36646782



  4. Marti H, Bommana S, Read TD, Pesch T, Prähauser B, Dean D, Borel N. Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants. Frontiers in microbiology 2021. PMID: 34276577


  5. Dean D, Swaminathan S, Kama M, Goemans S, Faktaufon D, Alnabelseya N, Spelke D, Kahrizi K, Black M, Mitra D. Development and Evaluation of a Point-of-Care Test in a Low-Resource Setting with High Rates of Chlamydia trachomatis Urogenital Infections in Fiji. Journal of clinical microbiology 2021. PMID: 33910964



  6. Bowden KE, Joseph SJ, Cartee JC, Ziklo N, Danavall D, Raphael BH, Read TD, Dean D. Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs. mSphere 2021. PMID: 33658279


  7. Choopara I, Suea-Ngam A, Teethaisong Y, Howes PD, Schmelcher M, Leelahavanichkul A, Thunyaharn S, Wongsawaeng D, deMello AJ, Dean D, Somboonna N. Fluorometric Paper-Based, Loop-Mediated Isothermal Amplification Devices for Quantitative Point-of-Care Detection of Methicillin-Resistant Staphylococcus aureus (MRSA). ACS sensors 2021. PMID: 33439634


  8. De Clercq E, Van Gils M, Schautteet K, Devriendt B, Kiekens C, Chiers K, Van Den Broeck W, Cox E, Dean D, Vanrompay D. Chlamydia trachomatis L2c Infection in a Porcine Model Produced Urogenital Pathology and Failed to Induce Protective Immune Responses Against Re-Infection. Frontiers in immunology 2020. PMID: 33193323




  9. Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T. Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo". mBio 2019. PMID: 31848290




  10. Pinsent A, Solomon AW, Bailey RL, Bid R, Cama A, Dean D, Goodhew B, Gwyn SE, Jack KR, Kandel RP, Kama M, Massae P, Macleod C, Mabey DCW, Migchelsen S, Müller A, Sandi F, Sokana O, Taoaba R, Tekeraoi R, Martin DL, White MT. The utility of serology for elimination surveillance of trachoma. Nature communications 2018. PMID: 30575720






  11. Smelov V, Vrbanac A, van Ess EF, Noz MP, Wan R, Eklund C, Morgan T, Shrier LA, Sanders B, Dillner J, de Vries HJC, Morre SA, Dean D. Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides. Frontiers in microbiology 2017. PMID: 29180986


  12. Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PloS one 2017. PMID: 28977025


  13. Turingan RS, Kaplun L, Krautz-Peterson G, Norsworthy S, Zolotova A, Joseph SJ, Read TD, Dean D, Tan E, Selden RF. Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay. PloS one 2017. PMID: 28562672


  14. Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PloS one 2017. PMID: 28410368



  15. Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D. Dynamics of genome change among Legionella species. Scientific Reports 2016. PMID: 27633769



  16. Gwyn S, Mitchell A, Dean D, Mkocha H, Handali S, Martin DL. Lateral flow-based antibody testing for Chlamydia trachomatis. Journal of immunological methods 2016. PMID: 27208400


  17. Recuero-Checa MA, Sharma M, Lau C, Watkins PA, Gaydos CA, Dean D. Chlamydia trachomatis growth and development requires the activity of host Long-chain Acyl-CoA Synthetases (ACSLs). Scientific Reports 2016. PMID: 26988341


  18. Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell reports 2016. PMID: 26774481



  19. Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, Del Rio C, Didelot X, Dillon JA, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD. Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ 2015. PMID: 25780762


  20. Batteiger BE, Wan R, Williams JA, He L, Ma A, Fortenberry JD, Dean D. Novel Chlamydia trachomatis strains in heterosexual sex partners, Indianapolis, Indiana, USA. Emerging infectious diseases 2014. PMID: 25340463



  21. Al-Kuhlani M, Rothschild J, Rothchild J, Pal S, de la Maza LM, Ouburg S, Morré SA, Dean D, Ojcius DM. TRAIL-R1 is a negative regulator of pro-inflammatory responses and modulates long-term sequelae resulting from Chlamydia trachomatis infections in humans. PloS one 2014. PMID: 24695582


  22. Dean D, Rothschild J, Ruettger A, Kandel RP, Sachse K. Zoonotic Chlamydiaceae species associated with trachoma, Nepal. Emerging infectious diseases 2013. PMID: 24274654



  23. Dean DA, Wadl PA, Hadziabdic D, Wang X, Trigiano RN. Analyzing microsatellites using the QIAxcel system. Methods in molecular biology (Clifton, N.J.) 2013. PMID: 23546795


  24. Wang A, Al-Kuhlani M, Johnston SC, Ojcius DM, Chou J, Dean D. Transcription factor complex AP-1 mediates inflammation initiated by Chlamydia pneumoniae infection. Cellular microbiology 2012. PMID: 23163821


  25. Dean D, Turingan RS, Thomann HU, Zolotova A, Rothschild J, Joseph SJ, Read TD, Tan E, Selden RF. A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis. PloS one 2012. PMID: 23272140


  26. Joseph SJ, Didelot X, Rothschild J, de Vries HJ, Morré SA, Read TD, Dean D. Population genomics of Chlamydia trachomatis: insights on drift, selection, recombination, and population structure. Molecular biology and evolution 2012. PMID: 22891032




  27. Trigiano RN, Wadl PA, Dean D, Hadziabdic D, Scheffler BE, Runge F, Telle S, Thines M, Ristaino J, Spring O. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycologia 2012. PMID: 22241615



  28. Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD. Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biology direct 2011. PMID: 21615910


  29. Somboonna N, Wan R, Ojcius DM, Pettengill MA, Joseph SJ, Chang A, Hsu R, Read TD, Dean D. Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages. mBio 2011. PMID: 21540364




  30. Wang A, Johnston SC, Chou J, Dean D. A systemic network for Chlamydia pneumoniae entry into human cells. Journal of bacteriology 2010. PMID: 20233927


  31. Dean D, Bruno WJ, Wan R, Gomes JP, Devignot S, Mehari T, de Vries HJ, Morré SA, Myers G, Read TD, Spratt BG. Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerging infectious diseases 2009. PMID: 19788805


  32. Tan C, Hsia RC, Shou H, Haggerty CL, Ness RB, Gaydos CA, Dean D, Scurlock AM, Wilson DP, Bavoil PM. Chlamydia trachomatis-infected patients display variable antibody profiles against the nine-member polymorphic membrane protein family. Infection and immunity 2009. PMID: 19487469


  33. Atik B, Skwor TA, Kandel RP, Sharma B, Adhikari HK, Steiner L, Erlich H, Dean D. Identification of novel single nucleotide polymorphisms in inflammatory genes as risk factors associated with trachomatous trichiasis. PloS one 2008. PMID: 18974840





  34. Nunes A, Gomes JP, Mead S, Florindo C, Correia H, Borrego MJ, Dean D. Comparative expression profiling of the Chlamydia trachomatis pmp gene family for clinical and reference strains. PloS one 2007. PMID: 17849007


  35. Dean D, Atik B, Ton TK, Vu QL, Lagree S. Evaluating the "A" component of the SAFE strategy. The Lancet. Infectious diseases 2007. PMID: 17182334


  36. Liu Z, Rank R, Kaltenboeck B, Magnino S, Dean D, Burall L, Plaut RD, Read TD, Myers G, Bavoil PM. Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae. Journal of bacteriology 2006. PMID: 17158668


  37. Gomes JP, Bruno WJ, Nunes A, Santos N, Florindo C, Borrego MJ, Dean D. Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots. Genome research 2006. PMID: 17090662


  38. Atik B, Thanh TT, Luong VQ, Lagree S, Dean D. Impact of annual targeted treatment on infectious trachoma and susceptibility to reinfection. JAMA 2006. PMID: 17003397





  39. Gomes JP, Borrego MJ, Atik B, Santo I, Azevedo J, Brito de Sá A, Nogueira P, Dean D. Correlating Chlamydia trachomatis infectious load with urogenital ecological success and disease pathogenesis. Microbes and infection 2005. PMID: 16289001




  40. Millman K, Black CM, Johnson RE, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S, Dean D. Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States. Journal of bacteriology 2004. PMID: 15060049





  41. Dean D, Neumayr L, Kelly DM, Ballas SK, Kleman K, Robertson S, Iyer RV, Ware RE, Koshy M, Rackoff WR, Pegelow CH, Waldron P, Benjamin L, Vichinsky E, Acute Chest Syndrome Study Group. Chlamydia pneumoniae and acute chest syndrome in patients with sickle cell disease. Journal of pediatric hematology/oncology 2003. PMID: 12544773